The composition and function of the human gut microbiome are closely linked with host health1. In addition to the predominant bacterial component, archaea are also among the commensal microorganisms inhabiting the human digestive tract. However, human-associated archaea and archaeal virome are often overlooked and remain unconsidered, since they are relatively low in abundance as compared to bacteria and mostly unculturable. As such, our research group is interested in understanding what archaea and archaeal viruses hiding in the human gut. Thus, we conducted a comprehensive analysis of the archaeal viruses in the human gut using the publicly available human gut metagenomic sequencing data.
First of all, we identified the human-associated archaeal genome contigs from 12 human microbial metagenomic datasets consisting of 3,971 samples from rural and urban human populations across 13 countries, resulting in 2,948 nonredundant archaeal genomic contigs. We assessed the prevalence of these archaea in the human populations, confirming that the archaea are prevalent in the human gut and expanding the archaeal diversity in the human gut.
Analysis of the CRISPR-Cas systems encoded by the archaea genomes revealed that 90% of archaea hold CRISPR loci, implying a rich archaeal virome2. Therefore, we further performed a comprehensive search for human gut archaeal viruses based on the archaeal CRISPR-spacer collection and the signatures of protein homology present in the archaeal viruses. We established a pipeline for archaeal viral detection and obtained 1,279 archaeal viral species in the human gut, of which, 95.2% infect Methanobrevibacteria_A, 56.5% share high identity (>95%) with the archaeal proviruses, 37.2% have a host range across archaeal species, and 55.7% are highly prevalent in the human population (>1%).
On the foundation of these archaeal viral species, we conducted a comprehensive analysis of the archaeal viruses in the human gut, showing that the archaeal viruses are widespread in the human gut ecosystem. We report the archaeal viruses related to virus origin, genome quality, functional annotation, taxonomic classification, biogeographic distribution, and host prediction. Among the viruses that can be assigned to viral taxonomy, the viral species that belong to the class Caudoviricetes (n = 389) (virus characterized by having tails and icosahedral capsids) are dominant, followed by the Cremevirales order (n = 13), and the Haloruvirales order (n =2); the Cremevirales viruses were predicted to infect M. intestinalis and Methanomassiliicoccus_A intestinalis, the Haloruvirales viruses were predicted to infect Haloferax massiliensis, while most of (305/388=78.6%) the Caudoviricetes species in HGAVD connected to the host of Methanobrevibacter_A smithii. The prevalence of these archaeal viral species is significantly distinct across different countries and the prevalence of a virus infecting Methanobrevibacter smithii reached 72.16% in the global human population.
These archaeal virus genomes encode an extensive function repertoire. In particular, in the analysis of 36 complete viral genomes, we observed that an archaeal virus-specific gene peiW and the genes (for integrase and MazE) in regulating the viral lysogenic-lytic cycle frequently occurred on these genomes, implying the dominance of temperate viruses in the human gut archaeal virome. We estimated that the fraction of these archaeal viruses in the human gut virome is around 0.50%, implying that there may be many archaeal viruses that remain unexplored. Considerable diversity of the unexplored archaeal viruses in the human gut and the novel archaeal viral species identified in this study can exactly fill in the gap in this field and serve as an expansion of the human gut archaeal viruses. Leveraging this comprehensive archaeal viral sequence collection, we provide unprecedented glimpses into the archaeal virome in the human gut, thus leading to a better understanding of the human gut ecosystem.
- Borrel, G., Brugère, J. F., Gribaldo, S., Schmitz, R. A. & Moissl-Eichinger, C. The host-associated archaeome. Nat Rev Microbiol(2020) doi:10.1038/s41579-020-0407-y.
- Sorek, R., Lawrence, C. M. & Wiedenheft, B. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annual Review of Biochemistryvol. 82 Preprint at https://doi.org/10.1146/annurev-biochem-072911-172315 (2013).